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- PDB-5tmc: Re-refinement of Thermus thermopiles DNA-directed RNA polymerase ... -

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Basic information

Entry
Database: PDB / ID: 5tmc
TitleRe-refinement of Thermus thermopiles DNA-directed RNA polymerase structure
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA polymerase sigma factor SigA
  • unknown protein
KeywordsTRANSFERASE / Symmetry Downshifting / Validation of Symmetry
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega ...Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / PHOSPHATE ION / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.71 Å
AuthorsWang, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural basis for transcription regulation by alarmone ppGpp.
Authors: Artsimovitch, I. / Patlan, V. / Sekine, S. / Vassylyeva, M.N. / Hosaka, T. / Ochi, K. / Yokoyama, S. / Vassylyev, D.G.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Other
Revision 1.2Feb 20, 2019Group: Data collection / Category: diffrn
Remark 0THIS ENTRY 5TMC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SMYSF ORIGINAL DATA ...THIS ENTRY 5TMC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SMYSF ORIGINAL DATA DETERMINED BY AUTHOR: I.ARTSIMOVITCH,V.PATLAN,S.SEKINE,M.N.VASSYLYEVA,T.HOSAKA, K.OCHI,S.YOKOYAMA,D.G.VASSYLYEV,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor SigA
Z: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,66515
Polymers430,7397
Non-polymers9268
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.350, 236.350, 249.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#1: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 35056.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11521.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q72ID6, UniProt: Q8RQE7*PLUS, DNA-directed RNA polymerase

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Protein / Protein/peptide , 2 types, 2 molecules FZ

#5: Protein RNA polymerase sigma factor SigA


Mass: 48568.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72L95, UniProt: Q5SKW1*PLUS
#6: Protein/peptide unknown protein


Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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Non-polymers , 5 types, 155 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.87 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1SMY.

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Data collection

DiffractionMean temperature: 100 K
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.875
11-H-K, K, -L20.125

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementResolution: 2.71→48.51 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. L-test and other twinning statistical tests have shown that the 1SMY data were partially twinned, but not perfectly twinned. With partial ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. L-test and other twinning statistical tests have shown that the 1SMY data were partially twinned, but not perfectly twinned. With partial twinning, the symmetry is partially upshifted to P6(5)22 from P6(5), which is consistent with the observed systematic absences and intensity merging R-factors reported for them. If the correct space group were P3(2), an up-shifted symmetry by a different twinning operation along the 3-fold axis could only generate P6(4), but not P6(5) because P3(2) is not a subgroup of P6(5). Moreover, the conversion of P3(2) to P6(5) using a perfect twinning method is not consistent with the L-test results, either, which suggests only a partial twinning, not perfect twinning. Given the problem of partial twinning in the data, model refinement was indeed very challenging. Six independent attempts of model refinement were made after proper crystallographic origin shift, starting with six different partial models according to the notes in author's notebook. All appear to have converged to similar crystallographic R-factor and free R-factor, even though the number of atoms in the final coordinates varied slightly among them. At the time of submission of this entry, the files for two of the six attempts have been located, but the remaining four files have not. It appears that there might be a mix-up in number of atoms among these files when reporting the number of atoms and R-factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 7528 3.7 %RANDOM
Rwork0.2651 ---
obs0.26588 198576 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.351 Å2
Baniso -1Baniso -2Baniso -3
1-22.66 Å20 Å20 Å2
2--22.66 Å20 Å2
3----45.32 Å2
Refinement stepCycle: 1 / Resolution: 2.71→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28225 0 47 147 28419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02228777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.98938925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51453579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78423.4381332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.512155176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.40115292
X-RAY DIFFRACTIONr_chiral_restr0.0850.24386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02121712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3547.517858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.5591028825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3121010919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2371510100
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.712→2.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 517 -
Rwork0.385 13602 -
obs--90.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24280.38490.32321.0702-0.31982.29120.03990.10390.049-0.05230.01380.04650.56510.1813-0.05370.76530.07560.0060.4972-0.0920.7208-7.333135.609-31.148
21.0523-0.74640.22750.9206-0.14850.8376-0.00740.09680.0551-0.16-0.04760.00130.1506-0.06690.0550.6348-0.0479-0.04790.5348-0.04580.6866-30.42159.402-43.38
31.17430.34141.24030.4270.77422.4740.10470.23160.13110.1045-0.04230.05690.42060.4692-0.06230.60590.1991-0.02310.6103-0.02390.6484.031145.3-26.383
42.71721.24571.23360.7714-0.49986.6268-0.0611-0.0521-0.1436-0.3977-0.2558-0.13581.90961.04280.31691.44261.0297-0.09860.8012-0.0210.518823.16122.106-7.435
50.2714-0.0563-0.11040.17060.06950.5314-0.04410.0070.08130.02090.01840.03120.14-0.00520.02580.6553-0.023-0.01030.50780.00310.8008-23.892146.939-11.987
60.2445-0.12950.03011.8691-0.43670.6819-0.042-0.11470.00240.10710.0318-0.0121-0.015-0.23630.01020.5227-0.0819-0.00940.59090.02740.7169-48.95162.4157.973
70.6089-0.4962-0.28960.72490.68510.85590.2380.04680.1054-0.173-0.1231-0.0891-0.2781-0.341-0.1150.76530.24690.08420.66860.09010.7111-61.054191.459-4.983
81.7397-0.43170.4844.1234-0.25210.61920.0746-0.0178-0.02910.6268-0.37170.4819-0.3653-0.04820.29711.02570.10480.14750.548-0.14450.4583-60.586189.40828.758
90.4088-0.1989-0.10420.193-0.2561.18880.06880.07180.0470.0161-0.0321-0.05540.1-0.1824-0.03670.593-0.0467-0.0390.5347-0.00570.7948-46.15161.582-19.056
101.64650.6386-0.25742.42151.04751.5133-0.17040.1260.2102-0.51390.02780.0698-0.49830.0650.14260.8446-0.0359-0.1170.43710.05260.6812-26.665194.957-32.878
110.11850.0206-0.13970.22180.08790.2588-0.03010.03090.0779-0.0950.01960.0433-0.0330.09110.01040.6755-0.0689-0.11680.50620.06770.8449-6.375199.14-4.963
120.15220.10560.08330.227-0.08710.5615-0.03570.01070.04380.0867-0.02790.0114-0.06110.030.06370.6084-0.0085-0.06180.5140.020.7893-3.612182.26527.973
130.2562-0.4237-0.34670.75520.45731.12640.07930.02540.0598-0.0304-0.0069-0.0191-0.0292-0.0132-0.07230.7352-0.0277-0.06470.45380.06360.7763-22.757218.68-2.142
141.3416-1.32240.76181.8502-0.10711.4251-0.0535-0.27060.04330.41550.192-0.1622-0.0164-0.1591-0.13851.0334-0.0406-0.09410.50550.05890.5365-20.953225.17430.73
151.967-1.71841.6332.3622-1.70331.47370.0424-0.29660.16440.5901-0.00150.4895-0.0056-0.0599-0.04091.46210.36260.5550.6764-0.04390.558-58.005258.1126.619
160.0315-0.04210.02810.0834-0.05380.0609-0.0553-0.0476-0.10080.2150.12810.1813-0.2056-0.0464-0.07281.02280.22080.34331.0483-0.01330.6127-78.003291.02932.515
176.59283.78931.10156.277-2.08853.72610.48640.3546-0.03741.4851-0.0482-0.197-0.6405-0.6088-0.43821.54050.2504-0.00010.73120.09060.3487-35.532257.87329.694
180.0635-0.15890.17811.0906-0.77871.022-0.0342-0.0050.0098-0.1032-0.07240.0699-0.01920.10070.10650.5825-0.0231-0.04140.53630.02440.8129-4.602178.005-13.064
190.066-0.18510.15560.8684-0.28751.26850.09710.03370.0774-0.04260.02410.03810.38620.187-0.12120.70150.1373-0.08150.5178-0.01240.77864.078141.792.794
200.7956-0.1361-0.27960.05350.0770.94060.1648-0.0770.00930.0229-0.0463-0.12740.1101-0.0892-0.11840.6257-0.06140.00210.50680.02770.7809-28.864149.82818.358
211.75050.9535-0.19640.62830.02480.1869-0.102-0.0716-0.007-0.26980.1335-0.0558-0.24360.2549-0.03150.588-0.1676-0.03980.70230.11170.78721.161187.454-9.924
220.37110.236-0.0332.03050.43430.7193-0.0861-0.0542-0.12010.26430.1008-0.0269-0.118-0.1359-0.01460.72820.0708-0.01460.54690.06860.6026-40.558241.7149.682
237.85152.67523.88663.5390.73772.08320.2673-0.14940.12480.2066-0.23460.20250.2444-0.0736-0.03260.8596-0.0285-0.07010.42630.06310.6794-49.283214.209-18.561
240.46940.1404-1.41450.3731-1.14188.84330.0831-0.0479-0.55540.0163-0.42680.0485-0.47470.29780.34370.7846-0.0087-0.21240.6490.01011.0617-25.832199.758-7.409
250.16010.05030.46010.04880.21481.4767-0.1089-0.0429-0.1067-0.01670.08220.1139-0.2680.03630.02661.07280.08270.06940.70180.26950.8185-2.083215.023-39.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION1A172 - 231
3X-RAY DIFFRACTION2A50 - 171
4X-RAY DIFFRACTION3B1 - 49
5X-RAY DIFFRACTION3B172 - 238
6X-RAY DIFFRACTION4B50 - 171
7X-RAY DIFFRACTION5C1 - 8
8X-RAY DIFFRACTION5C669 - 704
9X-RAY DIFFRACTION5C829 - 1004
10X-RAY DIFFRACTION6C9 - 16
11X-RAY DIFFRACTION6C390 - 540
12X-RAY DIFFRACTION7C17 - 142
13X-RAY DIFFRACTION7C324 - 389
14X-RAY DIFFRACTION8C143 - 323
15X-RAY DIFFRACTION9C541 - 668
16X-RAY DIFFRACTION10C705 - 828
17X-RAY DIFFRACTION11C1005 - 1119
18X-RAY DIFFRACTION12D2 - 11
19X-RAY DIFFRACTION12D1089 - 1481
20X-RAY DIFFRACTION13D12 - 100
21X-RAY DIFFRACTION13D514 - 617
22X-RAY DIFFRACTION14D111 - 164
23X-RAY DIFFRACTION14D449 - 513
24X-RAY DIFFRACTION15D165 - 216
25X-RAY DIFFRACTION15D340 - 396
26X-RAY DIFFRACTION16D217 - 339
27X-RAY DIFFRACTION17D397 - 448
28X-RAY DIFFRACTION18D618 - 776
29X-RAY DIFFRACTION19D777 - 946
30X-RAY DIFFRACTION20D947 - 1088
31X-RAY DIFFRACTION21E2 - 96
32X-RAY DIFFRACTION21D1482 - 1505
33X-RAY DIFFRACTION22F74 - 256
34X-RAY DIFFRACTION23F257 - 313
35X-RAY DIFFRACTION24F314 - 339
36X-RAY DIFFRACTION25F340 - 422

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Major update of PDB

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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